An automated Raman-based platform for the sorting of live cells by functional properties

doi:10.1038/s41564-019-0394-9

. 2019 Jun;4(6):1035-1048.

doi: 10.1038/s41564-019-0394-9. Epub 2019 Mar 18.

An automated Raman-based platform for the sorting of live cells by functional properties

Kang Soo Lee^{1

2}, Márton Palatinszky³, Fátima C Pereira³, Jen Nguyen^{1

2}, Vicente I Fernandez^{1

2}, Anna J Mueller³, Filippo Menolascina⁴, Holger Daims^{3

5}, David Berry³, Michael Wagner^{3

5}, Roman Stocker^{6

7}

Affiliations

¹ Ralph M. Parsons Laboratory for Environmental Science and Engineering, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
² Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland.
³ Center of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria.
⁴ School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh, UK.
⁵ The Comammox Research Platform, University of Vienna, Vienna, Austria.
⁶ Ralph M. Parsons Laboratory for Environmental Science and Engineering, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. romanstocker@ethz.ch.
⁷ Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland. romanstocker@ethz.ch.

PMID: 30886359
DOI: 10.1038/s41564-019-0394-9

An automated Raman-based platform for the sorting of live cells by functional properties

Kang Soo Lee et al. Nat Microbiol. 2019 Jun.

. 2019 Jun;4(6):1035-1048.

doi: 10.1038/s41564-019-0394-9. Epub 2019 Mar 18.

Authors

Affiliations

¹ Ralph M. Parsons Laboratory for Environmental Science and Engineering, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
² Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland.
³ Center of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria.
⁴ School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh, UK.
⁵ The Comammox Research Platform, University of Vienna, Vienna, Austria.
⁶ Ralph M. Parsons Laboratory for Environmental Science and Engineering, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. romanstocker@ethz.ch.
⁷ Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland. romanstocker@ethz.ch.

PMID: 30886359
DOI: 10.1038/s41564-019-0394-9

Erratum in

Publisher Correction: An automated Raman-based platform for the sorting of live cells by functional properties.
Lee KS, Palatinszky M, Pereira FC, Nguyen J, Fernandez VI, Mueller AJ, Menolascina F, Daims H, Berry D, Wagner M, Stocker R. Lee KS, et al. Nat Microbiol. 2019 May;4(5):902-903. doi: 10.1038/s41564-019-0446-1. Nat Microbiol. 2019. PMID: 30980037

Abstract

Stable-isotope probing is widely used to study the function of microbial taxa in their natural environment, but sorting of isotopically labelled microbial cells from complex samples for subsequent genomic analysis or cultivation is still in its early infancy. Here, we introduce an optofluidic platform for automated sorting of stable-isotope-probing-labelled microbial cells, combining microfluidics, optical tweezing and Raman microspectroscopy, which yields live cells suitable for subsequent single-cell genomics, mini-metagenomics or cultivation. We describe the design and optimization of this Raman-activated cell-sorting approach, illustrate its operation with four model bacteria (two intestinal, one soil and one marine) and demonstrate its high sorting accuracy (98.3 ± 1.7%), throughput (200-500 cells h^-1; 3.3-8.3 cells min^-1) and compatibility with cultivation. Application of this sorting approach for the metagenomic characterization of bacteria involved in mucin degradation in the mouse colon revealed a diverse consortium of bacteria, including several members of the underexplored family Muribaculaceae, highlighting both the complexity of this niche and the potential of Raman-activated cell sorting for identifying key players in targeted processes.

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Comment in

Raman-based sorting of microbial cells to link functions to their genes.
Lee KS, Wagner M, Stocker R. Lee KS, et al. Microb Cell. 2020 Feb 10;7(3):62-65. doi: 10.15698/mic2020.03.709. Microb Cell. 2020. PMID: 32161766 Free PMC article.

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References

1. Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431–437 (2013). - PubMed - DOI
1. Marcy, Y. et al. Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc. Natl Acad. Sci. USA 104, 11889–11894 (2007). - PubMed - DOI - PMC
1. Blainey, P. C. The future is now: single-cell genomics of bacteria and archaea. FEMS Microbiol. Rev. 37, 407–427 (2013). - PubMed - DOI
1. Xu, L., Brito, I. L., Alm, E. J. & Blainey, P. C. Virtual microfluidics for digital quantification and single-cell sequencing. Nat. Methods 13, 759–762 (2016). - PubMed - PMC - DOI
1. Ackermann, M. A functional perspective on phenotypic heterogeneity in microorganisms. Nat. Rev. Microbiol. 13, 497–508 (2015). - PubMed - DOI

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[1] Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431–437 (2013). - PubMed - DOI

[2] Rinke, C. et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431–437 (2013). - PubMed - DOI

[3] Marcy, Y. et al. Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc. Natl Acad. Sci. USA 104, 11889–11894 (2007). - PubMed - DOI - PMC

[4] Marcy, Y. et al. Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc. Natl Acad. Sci. USA 104, 11889–11894 (2007). - PubMed - DOI - PMC

[5] Blainey, P. C. The future is now: single-cell genomics of bacteria and archaea. FEMS Microbiol. Rev. 37, 407–427 (2013). - PubMed - DOI

[6] Blainey, P. C. The future is now: single-cell genomics of bacteria and archaea. FEMS Microbiol. Rev. 37, 407–427 (2013). - PubMed - DOI

[7] Xu, L., Brito, I. L., Alm, E. J. & Blainey, P. C. Virtual microfluidics for digital quantification and single-cell sequencing. Nat. Methods 13, 759–762 (2016). - PubMed - PMC - DOI

[8] Xu, L., Brito, I. L., Alm, E. J. & Blainey, P. C. Virtual microfluidics for digital quantification and single-cell sequencing. Nat. Methods 13, 759–762 (2016). - PubMed - PMC - DOI

[9] Ackermann, M. A functional perspective on phenotypic heterogeneity in microorganisms. Nat. Rev. Microbiol. 13, 497–508 (2015). - PubMed - DOI

[10] Ackermann, M. A functional perspective on phenotypic heterogeneity in microorganisms. Nat. Rev. Microbiol. 13, 497–508 (2015). - PubMed - DOI

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An automated Raman-based platform for the sorting of live cells by functional properties

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An automated Raman-based platform for the sorting of live cells by functional properties

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